lauantai 7. joulukuuta 2013

Testing 23andme's Ancestry Composition continues

I am happy to inform that 23andme has got repaired a few weird things I noticed two weeks ago.   Two Finns owning obviously non-Finnish European admixture show now sensible results.  The first one shows now 37% Finnish, being before the repair 100% Finnish.  A huge difference. The second Finn shows now 47,9%, was earlier 99.9% Finnish.   I was not cheating. 

What’s new

Basically Ancestry Composition is unchanged, only the software engine behind the user interface is revised.  Now it is time to go ahead and look at new results.  I have made some statistics.   The first graphics shows  results per country, how well 23andme has succeeded to assign people to their own national gene pool.     It was of course no sense to select national groups without own reference group, like Estonians.  They look “mixed” despite of the genetic diversity level.

All Finns with known recent foreign admix are excluded as well as Swedish speaking citizens, but of course I can’t know what happened hundreds years ago.   I can’t guarantee that all Finns are same people from the ice age and not even from the Roman Iron Age.   The Balts includes Lithianians and Latvians.The Russian group includes only ethnic Russians.

Secondly we see the standard deviation of results of each country.  It is good to notice that even in case the national proportion is very low, like in the case of Scandinavians, the deviation in own gene pool figures population diversity comparable to averagely higher country numbers.    This is one of those weird things being related to admix analyses and sometimes mislead people to think that admix analyses showing plenty of admixes means high diversity.   Actually it is a wrong conclusion.  Admixture results show only how much some corresponding part of your genome resembles the chosen reference set.    


Finnish results

Looking at results and the origin of Finns we can be sure that 23andme uses Finns from the late settlements in building the Finnish reference set.   The term late settlement is used by Finnish historians and means areas which were mostly populated during the Swedish era by administrative transactions (king’s orders) or by occupying areas in wars between Sweden and Novgorod/ later Moscow.   This means actually that the age of Finnish reference group is around 500-700 years and people living in older settlements, in areas that where populated pretty much before Swedish crusades to Finland,  are compared to them, not vice versa.   It is impossible to find out how much genes have during this 500-700 years period moved from old settlements to late settlements and how much from late settlements to old settlements, but we know the age of both populations .   The younger entity can’t be used to classify the older one.   Who populated the late settlements in Finland is another question.     

Anyway, evaluating the error caused by this poor test arrangement and putting things newly together we could try to estimate the lowest percentage for unmixed Finns by looking the Finnish history and personal data at 23andme.  It would be at lowest level around 70%, being somewhat below that in Southwestern Finland because they have given least genes to the late settlements, less than Tavastians, Karelians and Ostrobothnians.   In SW-Finland a bigger portion of old Finnish heritage remains unknown and hides inside nonspecific numbers.   You can notice this, as well as the Swedish admix level, just look at your shared Finnish results at Ancestry Composition.   The Finnish percentage being smaller than 70% we can expect some foreign admix more than the corresponding average Finnish admixture for example in Sweden and Russia.  
Some points more

Highest Finnish numbers seem to be from East Finland, near Iisalmi and Kuopio, highest in East Europe from Baltic countries, Pskov and Tverskaya regions in Russia and the highest Scandinavian number is from Värmland (Sic!), Sweden, followed by Norwegians nearby the Värmland on the other side of the boundary between Norway and Sweden. I wouldn't say I felt any déjà vu when looking these results, it is boring to see how admix analyses do this again.  Must say, we need now new ideas. Although 23andme uses obviously their own dedicated admix model they still fall into the same problem than all recent admix models deriving results based on a pure admix model and don't taking into account genetic drift. Unfortunately admix models conclude that the gene flow goes always from homogeneous populations to more heterogeneous one, without understanding the effect of genetic drift which happens usually after opposite gene flow. This happens because admix models don’t take into account timelines and believe that higher diversity is an admixture of present-day populations.

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